data_ADE
#
_chem_comp.id ADE
_chem_comp.name ADENINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H5 N5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ANE
_chem_comp.formula_weight 135.127
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code ADE
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1QD2
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
ADE N9 N9 N 0 1 Y N N N N N 14.713 -5.227 39.841 -0.655 -0.000 -2.079 N9 ADE 1
ADE C8 C8 C 0 1 Y N N N N N 15.960 -5.011 40.403 0.680 -0.000 -2.352 C8 ADE 2
ADE N7 N7 N 0 1 Y N N N N N 16.323 -3.740 40.420 1.360 -0.000 -1.242 N7 ADE 3
ADE C5 C5 C 0 1 Y N N N N N 15.266 -3.105 39.803 0.507 0.005 -0.190 C5 ADE 4
ADE C6 C6 C 0 1 Y N N N N N 15.126 -1.736 39.565 0.660 -0.000 1.205 C6 ADE 5
ADE N6 N6 N 0 1 N N N N N N 16.061 -0.802 39.828 1.919 -0.000 1.780 N6 ADE 6
ADE N1 N1 N 0 1 Y N N N N N 13.953 -1.315 39.047 -0.432 -0.000 1.962 N1 ADE 7
ADE C2 C2 C 0 1 Y N N N N N 12.997 -2.215 38.791 -1.637 -0.000 1.423 C2 ADE 8
ADE N3 N3 N 0 1 Y N N N N N 13.096 -3.534 38.955 -1.829 -0.000 0.121 N3 ADE 9
ADE C4 C4 C 0 1 Y N N N N N 14.252 -3.990 39.478 -0.796 -0.000 -0.715 C4 ADE 10
ADE HN9 HN9 H 0 1 N N N N N N 14.231 -6.117 39.719 -1.374 -0.000 -2.731 HN9 ADE 11
ADE H8 H8 H 0 1 N N N N N N 16.618 -5.797 40.809 1.110 -0.001 -3.342 H8 ADE 12
ADE HN61 1HN6 H 0 0 N N N N N N 15.958 0.197 39.654 2.012 -0.001 2.745 HN61 ADE 13
ADE HN62 2HN6 H 0 0 N N N N N N 16.911 -1.096 39.348 2.709 -0.004 1.217 HN62 ADE 14
ADE H2 H2 H 0 1 N N N N N N 12.035 -1.833 38.408 -2.498 0.000 2.075 H2 ADE 15
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
ADE N9 C8 SING Y N 1
ADE N9 C4 SING Y N 2
ADE N9 HN9 SING N N 3
ADE C8 N7 DOUB Y N 4
ADE C8 H8 SING N N 5
ADE N7 C5 SING Y N 6
ADE C5 C6 SING Y N 7
ADE C5 C4 DOUB Y N 8
ADE C6 N6 SING N N 9
ADE C6 N1 DOUB Y N 10
ADE N6 HN61 SING N N 11
ADE N6 HN62 SING N N 12
ADE N1 C2 SING Y N 13
ADE C2 N3 DOUB Y N 14
ADE C2 H2 SING N N 15
ADE N3 C4 SING Y N 16
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
ADE SMILES ACDLabs 10.04 n1c(c2ncnc2nc1)N
ADE SMILES_CANONICAL CACTVS 3.341 Nc1ncnc2[nH]cnc12
ADE SMILES CACTVS 3.341 Nc1ncnc2[nH]cnc12
ADE SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 c1[nH]c2c(n1)c(ncn2)N
ADE SMILES "OpenEye OEToolkits" 1.5.0 c1[nH]c2c(n1)c(ncn2)N
ADE InChI InChI 1.03 InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
ADE InChIKey InChI 1.03 GFFGJBXGBJISGV-UHFFFAOYSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
ADE "SYSTEMATIC NAME" ACDLabs 10.04 9H-purin-6-amine
ADE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 9H-purin-6-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
ADE 'Create component' 1999-07-08 RCSB
ADE 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id ADE
_pdbe_chem_comp_drugbank_details.drugbank_id DB00173
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Adenine
_pdbe_chem_comp_drugbank_details.description 'A purine base and a fundamental unit of adenine nucleotides.'
_pdbe_chem_comp_drugbank_details.cas_number 73-24-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action
'Adenine forms adenosine, a nucleoside, when attached to ribose, and deoxyadenosine when attached to deoxyribose, and it forms adenosine triphosphate (ATP), which drives many cellular metabolic processes by transferring chemical energy between reactions.'
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
ADE 6-Aminopurine DrugBank ?
ADE Adenin DrugBank ?
ADE Adenine DrugBank ?
ADE 'Vitamin B4' DrugBank ?
ADE Leuco-4 DrugBank 'International brand'
#
_pdbe_chem_comp_drugbank_classification.comp_id ADE
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00173
_pdbe_chem_comp_drugbank_classification.parent 6-aminopurines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Imidazopyrimidines
_pdbe_chem_comp_drugbank_classification.superclass 'Organoheterocyclic compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as 6-aminopurines. These are purines that carry an amino group at position 6. Purine is a bicyclic aromatic compound made up of a pyrimidine ring fused to an imidazole ring.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
ADE DB00173 'Adenine phosphoribosyltransferase' Humans P07741 unknown 1
ADE DB00173 "S-methyl-5'-thioadenosine phosphorylase" Humans Q13126 unknown 2
ADE DB00173 'Nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' Q05603 unknown 3
ADE DB00173 'Acetyl-CoA carboxylase 2' Humans O00763 unknown 4
ADE DB00173 'Low molecular weight phosphotyrosine protein phosphatase' Humans P24666 unknown 5
ADE DB00173 "5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase" 'Escherichia coli (strain K12)' P0AF12 unknown 6
ADE DB00173 'Peroxisomal trans-2-enoyl-CoA reductase' Humans Q9BY49 unknown 7
ADE DB00173 'Adenine DNA glycosylase' 'Escherichia coli (strain K12)' P17802 unknown 8
ADE DB00173 'Nucleoside 2-deoxyribosyltransferase' 'Lactobacillus helveticus' Q8RLY5 unknown 9
ADE DB00173 'SRSF protein kinase 2' Humans P78362 unknown 10
ADE DB00173 'Holliday junction ATP-dependent DNA helicase RuvB' 'Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)' Q5SL87 unknown 11
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
ADE N9 N 7.018 -2.190 1
ADE C8 C 7.893 -0.983 2
ADE N7 N 7.018 0.225 3
ADE C5 C 5.598 -0.233 4
ADE C6 C 4.299 0.517 5
ADE N6 N 4.299 2.018 6
ADE N1 N 3.000 -0.233 7
ADE C2 C 3.000 -1.732 8
ADE N3 N 4.299 -2.482 9
ADE C4 C 5.598 -1.732 10
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
ADE N9 C8 SINGLE NONE 1
ADE N9 C4 SINGLE NONE 2
ADE C8 N7 DOUBLE NONE 3
ADE N7 C5 SINGLE NONE 4
ADE C5 C6 SINGLE NONE 5
ADE C5 C4 DOUBLE NONE 6
ADE C6 N6 SINGLE NONE 7
ADE C6 N1 DOUBLE NONE 8
ADE N1 C2 SINGLE NONE 9
ADE C2 N3 DOUBLE NONE 10
ADE N3 C4 SINGLE NONE 11
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
ADE MurckoScaffold S1 scaffold 'c1ncc2nc[nH]c2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
ADE adenine F1 fragment 'Nc1ncnc2nc[nH]c12' InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10) GFFGJBXGBJISGV-UHFFFAOYSA-N
ADE imidazole F2 fragment 'c1c[nH]cn1' InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5) RAXXELZNTBOGNW-UHFFFAOYSA-N
ADE purine F3 fragment 'c1ncc2[nH]cnc2n1' InChI=1S/C5H4N4/c1-4-5(8-2-6-1)9-3-7-4/h1-3H,(H,6,7,8,9) KDCGOANMDULRCW-UHFFFAOYSA-N
ADE pyrimidine F4 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
ADE N9 S1 1
ADE C8 S1 1
ADE N7 S1 1
ADE C5 S1 1
ADE C6 S1 1
ADE N1 S1 1
ADE C2 S1 1
ADE N3 S1 1
ADE C4 S1 1
ADE N1 F1 1
ADE C6 F1 1
ADE C5 F1 1
ADE C4 F1 1
ADE N3 F1 1
ADE C2 F1 1
ADE N9 F1 1
ADE C8 F1 1
ADE N7 F1 1
ADE N6 F1 1
ADE C5 F2 1
ADE C4 F2 1
ADE N9 F2 1
ADE C8 F2 1
ADE N7 F2 1
ADE N7 F3 1
ADE C8 F3 1
ADE N9 F3 1
ADE C4 F3 1
ADE C5 F3 1
ADE C6 F3 1
ADE N1 F3 1
ADE C2 F3 1
ADE N3 F3 1
ADE C5 F4 1
ADE C6 F4 1
ADE N1 F4 1
ADE C2 F4 1
ADE N3 F4 1
ADE C4 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ADE
_pdbe_chem_comp_rdkit_properties.exactmw 135.054
_pdbe_chem_comp_rdkit_properties.amw 135.130
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 63.520
_pdbe_chem_comp_rdkit_properties.tpsa 80.480
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.874
_pdbe_chem_comp_rdkit_properties.CrippenMR 33.066
_pdbe_chem_comp_rdkit_properties.chi0v 4.736
_pdbe_chem_comp_rdkit_properties.chi1v 2.512
_pdbe_chem_comp_rdkit_properties.chi2v 1.053
_pdbe_chem_comp_rdkit_properties.chi3v 1.053
_pdbe_chem_comp_rdkit_properties.chi4v 0.626
_pdbe_chem_comp_rdkit_properties.chi0n 9.736
_pdbe_chem_comp_rdkit_properties.chi1n 4.854
_pdbe_chem_comp_rdkit_properties.chi2n 1.053
_pdbe_chem_comp_rdkit_properties.chi3n 1.053
_pdbe_chem_comp_rdkit_properties.chi4n 0.626
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.650
_pdbe_chem_comp_rdkit_properties.kappa1 2.191
_pdbe_chem_comp_rdkit_properties.kappa2 1.663
_pdbe_chem_comp_rdkit_properties.kappa3 0.540
_pdbe_chem_comp_rdkit_properties.Phi 0.364
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
ADE UniChem ChEMBL CHEMBL226345
ADE UniChem DrugBank DB00173
ADE UniChem PDBe ADE
ADE UniChem 'Guide to Pharmacology' 4788
ADE UniChem 'KEGG LIGAND' C00147
ADE UniChem ChEBI 16708
ADE UniChem ZINC ZINC000000000882
ADE UniChem eMolecules 27677487
ADE UniChem fdasrs JAC85A2161
ADE UniChem PharmGKB PA448048
ADE UniChem HMDB HMDB0000034
ADE UniChem Selleck adenine
ADE UniChem 'PubChem TPHARMA' 15970681
ADE UniChem NMRShiftDB 10016329
ADE UniChem Recon ade
ADE UniChem BindingDb 181146
ADE UniChem BindingDb 33218
ADE UniChem BindingDb 50228485
ADE UniChem 'EPA CompTox Dashboard' DTXSID6022557
ADE UniChem DrugCentral 89
ADE UniChem MetaboLights MTBLC16708
ADE UniChem BRENDA 13045
ADE UniChem BRENDA 144
ADE UniChem BRENDA 214750
ADE UniChem Rhea 16708
ADE UniChem ChemicalBook CB0406220
ADE UniChem ChemicalBook CB1323708
ADE UniChem DailyMed ADENINE
ADE UniChem ClinicalTrials ADENINE
ADE UniChem rxnorm ADENINE
ADE UniChem MedChemExpress HY-B0152
ADE UniChem 'Probes And Drugs' PD001577
ADE UniChem Nikkaji J5.257D
ADE UniChem eMolecules 474936
ADE UniChem eMolecules 533977
ADE UniChem SureChEMBL SCHEMBL8110
ADE UniChem 'PubChem TPHARMA' 14747713
ADE UniChem PubChem 190
ADE UniChem Mcule MCULE-6556342774
ADE UniChem ACTor 22051-90-7
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
ADE N9 2.214 0.152 0.443 ETKDGv3 1
ADE C8 1.945 -1.213 0.786 ETKDGv3 2
ADE N7 0.702 -1.564 0.615 ETKDGv3 3
ADE C5 0.076 -0.382 0.129 ETKDGv3 4
ADE C6 -1.324 -0.152 -0.247 ETKDGv3 5
ADE N6 -2.300 -1.189 -0.157 ETKDGv3 6
ADE N1 -1.655 1.040 -0.671 ETKDGv3 7
ADE C2 -0.676 2.105 -0.768 ETKDGv3 8
ADE N3 0.571 1.894 -0.431 ETKDGv3 9
ADE C4 0.937 0.591 0.033 ETKDGv3 10
ADE HN9 3.114 0.680 0.486 ETKDGv3 11
ADE H8 2.701 -1.895 1.153 ETKDGv3 12
ADE HN61 -3.291 -1.006 -0.430 ETKDGv3 13
ADE HN62 -2.035 -2.141 0.181 ETKDGv3 14
ADE H2 -0.979 3.081 -1.122 ETKDGv3 15
#